I returned from a similar trip in September 08 (only 4 months though!) from Ecuador to Brazil. With 6 months you will have plenty of time to see everything. We went at a relaxed pace and feel we covered pretty much everything apart from patagonia from the countries we visited (but we barely touched Brazil).
The following are not hidden gems by any means but they were the highlights of our trip!
The Galapagos Islands - the best place i have ever been. do not miss this as it is worth every penny!
Paraty, Brazil - stunning little colonial town with nice surrounding beaches.
We also loved Sucre in Bolivia, South West Bolivia / Salt flats, Mendoza and Lake District in argentina. Whale Watching in Puerto Madryn (Argentina), Banos and Cuenca in Ecuador, Trujillo and Arequipa in Peru. THe list could go on!
However it will depend what is happening when you are in some of these places. for example in Ecuador and Peru there was some sort of procession or parade almost every day. mostly schools or army bands but there was the excellent fiesta de Mama Negra in Latacunga and the Corpus christi procession we saw in Cuenca was very special. This type of thing can make some of the less well know places great. Chances are you will never know they are due to hapen until you hear some drums and look outside your hostel and see crowds and a procession marching or dancing down the street!!
As far as other things, as Darren mentioned Death Road is good fun. THe animal santuary we visited at the bottom was really nice and seemed well run, iguassu, machu pichu and of course cities like Rio and Buenos Aires largely live up to the hype but chances are they wont be the things you remember most - they certainly werent for us.
Enjoy - I'm very jealous now that i have returned to normality!
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